cnmodel.data package¶
cnmodel.data.connectivity¶
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 | # -*- encoding: utf-8 -*-
from ._db import add_table_data
#: Mouse synaptic convregence table
mouse_convergence = u"""
Convergence defines the average number of presynaptic cells of a particular
type (rows) that synapse onto a single postsynaptic cell of a particular
type (columns).
This connectivity matrix is currently incomplete.
Note: Bushy and pyramidal cells are known to have no (or very few)
collaterals within the CN, and so they are not listed as presynaptic cells in
this table. Octopus cells have collaterals (including in granule cell domains),
and should be added to this table when more data are available (Golding et al.,
J. Neurosci. 15: 3138, 1995)
----------------------------------------------------------------------------------------------
bushy tstellate dstellate octopus pyramidal tuberculoventral
sgc 3.3±0.6 [2] 6.5±1.0 [2] 35±0 [3] 60±0 [2] 48±0 [5] 24±0 [5]
dstellate 7 [1] 20 [1] 3 [1] 0 [4] 15 [5] 15 [5]
tstellate 0 [6] 0 [6] 0 [6] 0 [6] 0 [6] 0 [6]
tuberculoventral 6 6 0 0 [4] 21 [5] 0 [7]
pyramidal 0 0 0 0 0 0
----------------------------------------------------------------------------------------------
[1] Guesses based on Campagnola & Manis 2014
[2] Cao, X. & Oertel, D. (2010). Auditory nerve fibers excite targets through
synapses that vary in convergence, strength, and short-term plasticity.
Journal of Neurophysiology, 104(5), 2308–20.
Xie and Manis (unpublished): max EPSC = 3.4 ± 1.5 nA with ~0.3 nA steps
(Cao and Oertel, 2010) = ~11 AN inputs. However neither we nor Cao and Oertel
see that many clear steps in the responses, so use lower bound.
[3] Lower bound based on estimates from unpublished data Xie and Manis (2017)
Assumptions: No discernable step sizes when increasing shock intensity
at ANFs in radiate multipolars (dstellate)
Measured: 0.034 ± 15 nA sEPSC @ -70 mV
Measured: Maximal current from AN stim = 1.2 ± 0.7 nA @ -70 mV
Assuming that each AN provides 1 input, then N = ~35
[4] Octopus cells are devoid of inhibitory input (Golding et al., J. Neurosci., 1995)
[5] Convergence from Hancock and Voigt, Ann. Biomed. Eng. 27, 1999 and Zheng and Voigt,
Ann. Biomed. Eng., 34, 2006. Numbers are based on models for cat and gerbil,
respectively. Adjusted to 1/2 to avoid overexciting TV cells in network model.
[6] tstellate cells have collaterals within the CN. It has been proposed that they
provide auditory-driven input to the DCN (Oertel and Young, ), and also synapse
within the VCN (Oertel, SFN abstract). These parameters may need to be adjusted
once the convergence and strength is known.
[7] In the models of Hancock and Voigt (1999) and Zheng and Voigt (2006), the TV cells
have no connections with each other. However, Kuo et al. (J. Neurophysiol., 2015)
did see connections between pairs of TV cells in the mouse.
"""
add_table_data('convergence', row_key='pre_type', col_key='post_type',
species='mouse', data=mouse_convergence)
mouse_convergence_range = u"""
The convergence range table describes, for each type of connection from
presynaptic (rows) to postsynaptic (columns), the variance in frequency of
presynaptic cells relative to the postsynaptic cell.
All values are expressed as the sigma for a lognormal distribution scaled to
the CF of the postsynaptic cell.
----------------------------------------------------------------------------------------------
bushy tstellate dstellate octopus pyramidal tuberculoventral
sgc 0.05 [1] 0.1 [1] 0.4 [1] 0.5 [5] 0.1 [1] 0.1 [1]
dstellate 0.208 [2] 0.347 [2] 0.5 [1] 0 0.2 [1] 0.2 [1]
tstellate 0.1 [4] 0.1 [4] 0 0 0 0
tuberculoventral 0.069 [3] 0.111 [3] 0 0 0.15 [1] 0
pyramidal 0 0 0 0 0 0
----------------------------------------------------------------------------------------------
[1] Guess based on axonal / dendritic morphology.
[2] Calculated from Campagnola & Manis 2014 fig. 7C
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to
get the sigma for a lognormal distribution.
DS->Bushy: ln(2) * 0.3 = 0.208
DS->TStellate: ln(2) * 0.5 = 0.347
[3] Calculated from Campagnola & Manis 2014 fig. 9C
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to
get the sigma for a lognormal distribution.
TV->Bushy: ln(2) * 0.10 = 0.069
TV->TStellate: ln(2) * 0.16 = 0.111
[4] Guess based on very limited information in Campagnola & Manis 2014 fig. 12
[5] Octopus cells get a wide range of ANF input (but weak on a per input basis)
For example, see McGinley et al., 2012 or Spencer et al., 2012.
"""
add_table_data('convergence_range', row_key='pre_type', col_key='post_type',
species='mouse', data=mouse_convergence_range)
#--------------------------------------------------------------------------------------------
guineapig_convergence = u"""
Convergence defines the average number of presynaptic cells of a particular
type (rows) that synapse onto a single postsynaptic cell of a particular
type (columns).
This connectivity matrix is currently incomplete.
Note: Bushy and pyramidal cells are known to have no (or very few)
collaterals within the CN, and so they are not listed as presynaptic cells in
this table. Octopus cells have collaterals (including in granule cell domains),
and should be added to this table when more data are available (Golding et al.,
J. Neurosci. 15: 3138, 1995)
This table is just a guess... using mouse data...
----------------------------------------------------------------------------------------------
bushy tstellate dstellate octopus pyramidal tuberculoventral mso
sgc 3.3±0.6 [2] 6.5±1.0 [2] 35±0 [3] 60±0 [2] 48±0 [5] 24±0 [5] 0
bushy 0 0 0 0 0 0 12 [8]
dstellate 7 [1] 20 [1] 3 [1] 0 [4] 15 [5] 15 [5] 0
tstellate 0 [6] 0 [6] 0 [6] 0 [6] 0 [6] 0 [6] 0
tuberculoventral 6 6 0 0 [4] 21 [5] 0 [7] 0
pyramidal 0 0 0 0 0 0 0
----------------------------------------------------------------------------------------------
[1] Guesses based on Campagnola & Manis 2014 (using mouse data on guinea pig cells)
[2] Cao, X. & Oertel, D. (2010). Auditory nerve fibers excite targets through
synapses that vary in convergence, strength, and short-term plasticity.
Journal of Neurophysiology, 104(5), 2308–20.
Xie and Manis (unpublished): max EPSC = 3.4 ± 1.5 nA with ~0.3 nA steps
(Cao and Oertel, 2010) = ~11 AN inputs. However neither we nor Cao and Oertel
see that many clear steps in the responses, so use lower bound.
[3] Lower bound based on estimates from unpublished data Xie and Manis (2017)
Assumptions: No discernable step sizes when increasing shock intensity
at ANFs in radiate multipolars (dstellate)
Measured: 0.034 ± 15 nA sEPSC @ -70 mV
Measured: Maximal current from AN stim = 1.2 ± 0.7 nA @ -70 mV
Assuming that each AN provides 1 input, then N = ~35
[4] Octopus cells are devoid of inhibitory input (Golding et al., J. Neurosci., 1995)
[5] Convergence from Hancock and Voigt, Ann. Biomed. Eng. 27, 1999 and Zheng and Voigt,
Ann. Biomed. Eng., 34, 2006. Numbers are based on models for cat and gerbil,
respectively. Adjusted to 1/2 to avoid overexciting TV cells in network model.
[6] tstellate cells have collaterals within the CN. It has been proposed that they
provide auditory-driven input to the DCN (Oertel and Young, ), and also synapse
within the VCN (Oertel, SFN abstract). These parameters may need to be adjusted
once the convergence and strength is known.
[7] In the models of Hancock and Voigt (1999) and Zheng and Voigt (2006), the TV cells
have no connections with each other. However, Kuo et al. (J. Neurophysiol., 2015)
did see connections between pairs of TV cells in the mouse.
[8] Bushy convergence to MSO is a guess
"""
add_table_data('convergence', row_key='pre_type', col_key='post_type',
species='guineapig', data=guineapig_convergence)
guineapig_convergence_range = u"""
The convergence range table describes, for each type of connection from
presynaptic (rows) to postsynaptic (columns), the variance in frequency of
presynaptic cells relative to the postsynaptic cell.
All values are expressed as the sigma for a lognormal distribution scaled to
the CF of the postsynaptic cell.
*** This table is just a guess - using data from mouse... ****
-------------------------------------------------------------------------------------------------------
bushy tstellate dstellate octopus pyramidal tuberculoventral mso
sgc 0.05 [1] 0.1 [1] 0.4 [1] 0.5 [5] 0.1 [1] 0.1 [1] 0
bushy 0 0 0 0 0 0 0.05 [6]
dstellate 0.208 [2] 0.347 [2] 0.5 [1] 0 0.2 [1] 0.2 [1] 0
tstellate 0.1 [4] 0.1 [4] 0 0 0 0 0
tuberculoventral 0.069 [3] 0.111 [3] 0 0 0.15 [1] 0 0
pyramidal 0 0 0 0 0 0 0
--------------------------------------------------------------------------------------------------------
[1] Guess based on axonal / dendritic morphology.
[2] Calculated from Campagnola & Manis 2014 fig. 7C (Using mouse data on guinea pig cells)
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to
get the sigma for a lognormal distribution.
DS->Bushy: ln(2) * 0.3 = 0.208
DS->TStellate: ln(2) * 0.5 = 0.347
[3] Calculated from Campagnola & Manis 2014 fig. 9C (Using mouse data on guinea pig cells)
Distribution widths are given in stdev(octaves), so we multiply by ln(2) to
get the sigma for a lognormal distribution.
TV->Bushy: ln(2) * 0.10 = 0.069
TV->TStellate: ln(2) * 0.16 = 0.111
[4] Guess based on very limited information in Campagnola & Manis 2014 fig. 12
[5] Octopus cells get a wide range of ANF input (but weak on a per input basis)
For example, see McGinley et al., 2012 or Spencer et al., 2012.
[6] MSO convergence from bushy cells is a guess.
"""
add_table_data('convergence_range', row_key='pre_type', col_key='post_type',
species='guineapig', data=guineapig_convergence_range)
|
cnmodel.data.synapses¶
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 | # -*- encoding: utf-8 -*-
from ._db import add_table_data
add_table_data('sgc_synapse', row_key='field', col_key='post_type',
species='mouse', data=u"""
AMPA_gmax and NMDA_gmax are the estimated average peak conductances (in nS)
resulting from an action potential in a single auditory nerve terminal, under
conditions that minimize the effects of short-term plasticity.
AMPA_gmax are from values measured at -65 mV (or -70mV), and represent SINGLE TERMINAL
conductances
AMPAR_gmax are the individual synapse postsynaptic conductance
NMDA_gmax values are taken as the fraction of the current that is NMDAR dependent
at +40 mV (see below)
n_rsites is the number of release sites per SGC terminal.
-----------------------------------------------------------------------------------------------------------------------------------
bushy tstellate dstellate octopus pyramidal tuberculoventral
AMPA_gmax 21.05±15.4 [1] 4.6±3.1 [2] 0.49±0.29 [7] 0.87±0.23 [3] 1.8±1.05 [8] 2.2±1.5 [8]
AMPAR_gmax 4.6516398 [10] 4.632848 [10] 1.7587450 [10] 16.975147 [10] 1.8 [8] 2.2 [8]
NMDA_gmax 10.8±4.6 [1] 2.4±1.6 [2] 0.552±0.322 [7] 0.17±0.046 [3] 0.8±0.66 [8] 2.4±1.6 [8]
NMDAR_gmax 0.4531933 [10] 1.2127097 [10] 0.9960820 [10] 0.6562702 [10] 0.4 [8] 1.2127097 [8]
EPSC_cv 0.12 [8] 0.499759 [9] 0.886406 [9] 1.393382 [9] 0.499 [8] 0.499 [8]
Pr 1.000 [11] 1.000 [11] 1.000 [11] 1.000 [11] 1.000 [8] 1.000 [8]
n_rsites 100 [5] 4 [6] 1 [4] 1 [4] 2 [8] 2 [8]
weight 0.027 [12] 0.006 [12] 0.00064 [12] 0.0011 [12] 0.0023 [12] 0.0029 [12]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Derived from Cao, X. & Oertel, D. (2010). Single-terminal conductance was
reported as 21.5±15.4 nS (1.4±1.0 nA at -65 mV). The ratio of NMDA current to
total current is 0.3, so AMPA and NMDA currents are:
AMPA_gmax = 21.5±15.4 nS (measured at -65 mV)
NMDA_gmax = 21.5±15.4 nS * 0.3 = 10.8±4.6 nS
Age>p17, Temperature=33C, [Mg2+]=1.3mM, [Ca2+]=2.4mM
Units are nS.
[2] Derived from Cao, X. & Oertel, D. (2010). Single-terminal conductance was
estimated as 4.6±3.1 nS. The ratio of NMDA current to
total current is 0.53, so AMPA and NMDA currents are:
AMPA_gmax = 4.6±3.1 nS
NMDA_gmax = 4.6±3.1 nS * 0.53 = 2.4±1.6 nS
Estimated number of inputs per AN fiber:
0.3 nA step, 0.08 nA mini size = ~ 4 inputs per AN fiber
Age>p17, Temperature=33C, [Mg2+]=1.3mM, [Ca2+]=2.4mM
Units are nS
[3] Derived from Cao, X. & Oertel, D. (2010). Single-terminal conductance was
estimated as 52±14 nS / 60 = 0.87±0.23 nS. The ratio of NMDA current to
total current is 0.2, so AMPA and NMDA currents are:
AMPA_gmax = 0.87±0.23 nS
NMDA_gmax = 0.87±0.23 nS * 0.2 = 0.17±0.046 nS
Age>p17, Temperature=33C, [Mg2+]=1.3mM, [Ca2+]=2.4mM
Units are nS
[4] Assumption based on mini size and lack of discernable EPSC step (guess).
Should be verified.
[5] Oleskevich & Walmsley ~2002, Wang & Manis 2005. Units are nS
[6] A value of 45 would be chosen to satisfy the CV of EPSC amplitude determined in [9].
However, those measures are for simultaneous stimulation of multiple AN fibers.
A value of 4 is included here to correspond to measures in Cao and Oertel (2010)
(see note [2])
[7] (Xie and Manis, Frontiers in Neural Circuits, 2017):
Measurements from CBA/CaJ mouse "radiate" multipolar cells in the AVCN.
Single terminal conductance = (1.2 ± 0.70 nA/70 mV)/ 35 inputs = 0.490 ± 0.286 nS
(see connections.py)
Single terminal conductance from mini = 34 pA/70 mV = 0.486 nS (single mini)
Assume same AMPA/NMDA ratio as tstellate cells, but measures made where NMDA = 0
(at negative V):
AMPA_gmax = 0.490±0.286 nS
NMDA_gmax = 0.490±0.286 nS * 0.53/0.47 = 0.552±0.322 nS
Age > P35, Temperature=34C, [Mg2+]=1.5mM, [Ca2+]=2.5mM
[8] Thin air. These are for testing the software, not necessarily for performing
real simulations. Note: Pyramidal cell strength has been reduced
because of large convergence and high input resistance of the reference cell model.
[9] Reanalysis of evoked EPSCs in stellate cells (Manis/Xie, 2014)
[10] Maximum AMPA open conductance per synaptic site (units are pS).
These values are calculated by running python cnmodel/synapses/tests/test_psd.py
for a specific cell type (if the cell uses the receptor mechanisms; this is
not necessary for simple exp2syn style mechanisms)
to ensure that maximum AMPA conductance during PSG matches [1, 2 or 3]
For a bushy cell, the original default values (bushy cell) were:
AMPAR_gmax 3.314707700918133
NMDAR_gmax 0.4531929783503451
These values will also depend on the number of release sites per
synapse (the total conductance is produce of site gmax and nsites).
A note on the precision of these values: This precision is only
required for the tests of the model, as a way of ensuring numerical
equivalency after potential modifications of the code. The precision
of the value is in no way intended to specificy biological precision.
For example, a change in the rate constants in the AMPA_Trussell AMPA
receptor model could (and probably would) change the open probability,
and therefore the maximal conductance of an EPSC. However, as this is
only a representation of the EPSC, the "receptor" conductance should
be scaled so that the computed EPSC has the same maximal conductance
as prior to the kinetic modifications. Because the receptor model is
numerically computed (and not analytically tractable without
additional knowledge of the ligand time course), a numerical solution
is required.
[11] Pr is the initial release probability. The value can be computed by
setting Pr to 1 in this file, and running the cnmodel test_synapses.py
with the appropriate presynaptic source and postsynaptic target,
once all other parameters are set. The Pr is used to rescale
the AMPAR_gmax so that the total current matches the data in
AMPA_gmax in the table (on average).
[12] weight is the weight to use in a netcon object (NEURON) for "simple"
synapses based on the exp2syn mechanism. These are ~ AMPAR_gmax *
0.065*2e-2, to approximate the current injected by the multisite
synapse.
""")
add_table_data('sgc_ampa_kinetics', row_key='field', col_key='post_type',
species='mouse', data=u"""
AMPA receptor kinetic values obtained by fitting the model of Raman and
Trussell (1992) to measured EPSCs in the mouse VCN.
Ro1, Ro2, Rc1, Rc2, and PA are kinetic constants affecting the AMPA receptor
mechanism. tau_g and A affect the speed and amplitude of transmitter release
(implemented in the presynaptic release mechanism).
These parameters were selected to fit the model output to known EPSC shapes.
PA is a polyamine block parameter ued in the AMPAR mechanism (concentration in micromolar).
------------------------------------------------------------------------------------------------
bushy tstellate dstellate pyramidal octopus tuberculoventral mso
Ro1 107.85 [4] 39.25 [4] 39.25 [7] 39.25 [4] 107.85 [5] 39.25 [7] 107.85 [4]
Ro2 0.6193 [4] 4.40 [4] 4.40 [7] 4.40 [4] 0.6193 [5] 4.40 [7] 0.6193 [4]
Rc1 3.678 [4] 0.667 [4] 0.667 [7] 0.667 [4] 3.678 [5] 0.667 [7] 3.678 [4]
Rc2 0.3212 [4] 0.237 [4] 0.237 [7] 0.237 [4] 0.3212 [5] 0.237 [7] 0.3212 [4]
tau_g 0.10 [4] 0.25 [4] 0.25 [7] 0.25 [4] 0.10 [5] 0.25 [4] 0.10 [4]
amp_g 0.770 [4] 1.56625 [4] 1.56625 [7] 1.56625 [4] 0.770 [5] 1.56625 [4] 0.770 [4]
PA 45 [12] 0.1 [12] 0.1 [7] 0.1 [12] 45 [5] 0.1 [7] 45 [12]
------------------------------------------------------------------------------------------------
[4] Xie & Manis 2013, Table 2
[5] copied from bushy cells; no direct data.
[7] Data copied from t-stellate column (no literature on these cells). Unpublished data suggests these
should be slightly different, but is complicated by electrotonically distant synaptic sites that
preclude accurate measurement of kinetics.
[12] Wang & Manis (unpublished)
""")
add_table_data('sgc_epsp_kinetics', row_key='field', col_key='post_type',
species='mouse', data=u"""
EPSC shape parameters obtained from fits of Xie & Manis 2013 Equation 3 to measured EPSCs.
------------------------------------------------------------------------------------------------
bushy tstellate dstellate pyramidal octopus tuberculoventral
tau_r 0.253 [11] 0.19 [11] 0.253 [13]
tau_f 0.16 [11] 1.073 [11] 0.16 [13]
tau_s 0.765 [11] 3.3082 [11] 0.765 [13]
F 0.984 [11] 0.917 [11] 0.984 [13]
------------------------------------------------------------------------------------------------
[11] Xie & Manis 2013, Table 3
[13] Copied from bushy cells; no direct data
""")
add_table_data('sgc_release_dynamics', row_key='field', col_key='post_type',
species='mouse', data=u"""
Kinetic parameters correspond to variables as described by Dittman et al.
(2000), their Table 1.
F: ~ Resting release probability
------------------------------------------------------------------------------------------------
bushy tstellate dstellate pyramidal octopus tuberculoventral
F 0.29366 [1] 0.43435 [1] 0.43435 [2] 0.43435 [1] 0.29366 [14] 0.43435 [1]
k0 0.52313 [1] 0.06717 [1] 0.06717 [2] 0.06717 [1] 0.52313 [14] 0.06717 [1]
kmax 19.33805 [1] 52.82713 [1] 52.82713 [2] 52.82713 [1] 19.33805 [14] 52.82713 [1]
kd 0.11283 [1] 0.08209 [1] 0.08209 [2] 0.08209 [1] 0.11283 [14] 0.08209 [1]
ks 11.531 [1] 14.24460 [1] 14.24460 [2] 14.24460 [1] 11.531 [14] 14.24460 [1]
kf 17.78 [1] 18.16292 [1] 18.16292 [2] 18.16292 [1] 17.78 [14] 18.16292 [1]
taud 15.16 [1] 3.98 [1] 3.98 [2] 3.98 [1] 15.16 [14] 3.98 [1]
taus 17912.2 [1] 16917.120 [1] 16917.120 [2] 16917.120 [1] 17912.2 [14] 16917.120 [1]
tauf 9.75 [1] 11.38 [1] 11.38 [2] 11.38 [1] 9.75 [14] 11.38 [1]
dD 0.57771 [1] 2.46535 [1] 2.46535 [2] 2.46535 [1] 0.57771 [14] 2.46535 [1]
dF 0.60364 [1] 1.44543 [1] 1.44543 [2] 1.44543 [1] 0.60364 [14] 1.44543 [1]
------------------------------------------------------------------------------------------------
[1] Xie & Manis 2013, Table 1. Although independently measured in > P30 CBA/CaJ mice,
the values are similar to the measurements from Yang and Xu-Friedman, 2008
in P14-P21 CBA/CaJ mice.
[2] Data copied from t-stellate column (no literature on these cells)
[14] Data copied from bushy cell column (no literature on these cells)
""")
add_table_data('gly_kinetics', row_key='field', col_key='post_type',
species='mouse', data=u"""
Kinetic parameters for glycine receptor mechanisms.
These are currently used for both DS and TV synapses, but should probably be
separated in the future.
KV, KU, and XMax are kinetic parameters for the cleft transmitter mechanism.
------------------------------------------------------------------------------------------------
bushy tstellate dstellate pyramidal tuberculoventral
KV 1e9 [1] 531.0 [1] 531.0 [1] 531.0 [2] 531.0 [2]
KU 4.46 [1] 4.17 [1] 4.17 [1] 4.17 [2] 4.17 [2]
XMax 0.733 [1] 0.731 [1] 0.731 [1] 0.731 [2] 0.731 [2]
------------------------------------------------------------------------------------------------
[1] Xie & Manis 2013
[2] Copied from tstellate data (Kuo et al., J. Neurophysiol. indicate glycinergic IPSCs in TV
and pyramidal cells are fast, with a decay time constant similar to that seen in tstellate
cells). In pyramidal cells, this is consistent with the brief cross-correlation tip (Voigt
and Young, 1980) and brief somatic current source (Manis and Brownell, 1983).
""")
# Mouse data
# TV conductance onto pyr cells: 2.1 nS SD 2.9 nS (Kuo et al., 2012)
# TV conductance onto TV cells: 1.8 ns SD 2.3 nS.
#
add_table_data('bushy_synapse', row_key='field', col_key='post_type',
species='mouse', data=u"""
AMPA_gmax and NMDA_gmax are the estimated average peak conductances (in nS)
resulting from an action potential in a single presynaptic terminal under
conditions that minimize the effects of short-term plasticity.
AMPA_gmax are from values measured at -65 mV (or -70mV), and represent SINGLE TERMINAL
conductances
AMPAR_gmax are the individual synapse postsynaptic conductance
NMDA_gmax values are taken as the fraction of the current that is NMDAR dependent
at +40 mV (see below)
n_rsites is the number of release sites per terminal.
-----------------------------------------------------------------------------------------------------------------------------------
mso
AMPA_gmax 21.05±15.4 [1]
AMPAR_gmax 4.6516398 [2]
NMDA_gmax 0 [3]
NMDAR_gmax 0 [3]
EPSC_cv 0.12 [4]
Pr 1.000 [5]
n_rsites 36 [6]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Taken from the mouse bushy cell model.
Units are nS.
[2] See note [10] for the SGC-bushy synapse
[3] Assume no NMDA receptors at this synapse
[4] See SGC-bushy synapse
[5] Just to scale with the multisite synapse model
[6] This is a guess.
""")
|
cnmodel.data.populations¶
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | # -*- encoding: utf-8 -*-
from ._db import add_table_data
add_table_data('populations', row_key='field', col_key='cell_type',
species='mouse', data=u"""
-----------------------------------------------------------------------------------------------------
sgc bushy tstellate dstellate octopus pyramidal tuberculoventral
n_cells 10000 [1] 6500 [2] 6500 [2] 650 [3] 5000 3000 5000
cf_min 2000 2000 2000 2000 2000 2000 2000
cf_max 90000 90000 90000 90000 90000 90000 90000
-----------------------------------------------------------------------------------------------------
[1] ?
[2] Rough estimate from allen brain atlas data:
Volume of VCN is 0.377 mm^3, by counting voxels with 'VCO' (101) label in Common Coordinate Framework atlas.
753370 voxels * 0.5 * 10e-6**3 m^3/vox = 0.377 mm^3
Counted Slc17a7 (pan-excitatory) cell bodies in a 500x500 um chunk of VCN
http://mouse.brain-map.org/experiment/siv?id=69014470&imageId=68856767&initImage=ish&coordSystem=pixel&x=7616.5&y=4144.5&z=1
266 cells in 500x500 um = 34707 cells / mm^2
34707**3/2 * 0.377 mm^3 = 13084 cells total
Assume half are bushy, half are T-stellate
[3] Rough estimate from allen brain atlas data:
Similar to [2], using Gad1 inhibitory marker
http://mouse.brain-map.org/experiment/siv?id=75492764&imageId=75405134&initImage=ish&coordSystem=pixel&x=5320.5&y=3232.5&z=1
36 cells in 500x500 um = 144e6 / m^2 ~= 1728 / mm^2
= 651 cells total (VCN, unilateral)
""")
|
cnmodel.data.ionchannels¶
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from ._db import add_table_data
"""
Ion channel density tables
All of the ion channel densities for the models implemented in cnmodel
are (or should be) stated here, and should not be modified in the
cnmodel code itself.
"""
add_table_data('RM03_channels', row_key='field', col_key='cell_type',
species='guineapig', data=u"""
This table describes the ion channel densities (and voltage shifts if necessary)
for different cell types in the original Rothman Manis 2003 model.
Data from Table 1, except for "octopus" cells, which is modified (see note 3)
-----------------------------------------------------------------------------------------------------------------------------------
bushy-II bushy-II-I tstellate tstellate-t bushy-I-II octopus
RM03_name II II-I I-c I-t I-II II-o [4]
soma_na_gbar 1000. [1] 1000. [1] 1000. [1] 1000. [1] 1000. [2] 1000. [3]
soma_kht_gbar 150.0 [1] 150.0 [1] 150.0 [1] 80.0 [1] 150.0 [2] 150.0 [3]
soma_klt_gbar 200.0 [1] 35.0 [1] 0.0 [1] 0.0 [1] 20.0 [2] 1000. [3]
soma_ka_gbar 0.0 [1] 0.0 [1] 0.0 [1] 65.0 [1] 0.0 [2] 0.0 [3]
soma_ih_gbar 20.0 [1] 3.5 [1] 0.5 [1] 0.5 [1] 2.0 [2] 30.0 [3]
soma_leak_gbar 2.0 [1] 2.0 [1] 2.0 [1] 2.0 [1] 2.0 [2] 2.0 [3]
soma_leak_erev -65 [1] -65 [1] -65 [1] -65 [1] -65 [2] -65 [3]
soma_na_type nacn [1] nacn [1] nacn [1] nacn [1] nacn [2] nacn [3]
soma_ih_type ihvcn [1] ihvcn [1] ihvcn [1] ihvcn [1] ihvcn [2] ihvcn [3]
soma_Cap 12.0 [1] 12.0 [1] 12.0 [1] 12.0 [1] 12.0 [2] 25.0 [3]
soma_e_k -84 [1] -84 [1] -84 [1] -84 [2] -84 [2] -84 [2]
soma_e_na 50. [1] 50. [1] 50. [1] 50. [2] 50. [2] 50. [2]
soma_ih_eh -43 [1] -43 [1] -43 [1] -43 [2] -43 [2] -43 [2]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Rothman and Manis, 2003
Age "adult", Temperature=22C
Units are nS.
[2] Rothman and manis, 2003, model I-II
Some low-voltage K current, based on observations of
a single spike near threshold and regular firing for higher
currents (Xie and Manis, 2017)
[3] Derived from Rothman and Manis, 2003, model II
Large amounts of low-voltage K current, and elevated HCN. Conductances
based on Rothman and Manis, 2003; concept from Cao and Oertel
[4] Designation for elevated LTK and Ih for octopus cells
""")
add_table_data('XM13_channels', row_key='field', col_key='cell_type',
species='mouse', data=u"""
This table describes the ion channel densities (and voltage shifts if necessary)
for different cell types based on the Xie and Manis 2013 models for mouse.
-----------------------------------------------------------------------------------------------------------------------------------
bushy-II bushy-II-I tstellate bushy-I-II
XM13_name II II-I I-c I-II
soma_na_gbar 1000. [1] 1000. [1] 3000. [1] 1000. [2]
soma_kht_gbar 58.0 [1] 58.0 [1] 500.0 [1] 150.0 [2]
soma_klt_gbar 80.0 [1] 14.0 [1] 0.0 [1] 20.0 [2]
soma_ka_gbar 0.0 [1] 0.0 [1] 0.0 [1] 0.0 [2]
soma_ih_gbar 30.0 [1] 30.0 [1] 18.0 [1] 2.0 [2]
soma_leak_gbar 2.0 [1] 2.0 [1] 8.0 [1] 2.0 [2]
soma_leak_erev -65 [1] -65 [1] -65 [1] -65 [2]
soma_na_type nacn [1] nacn [1] nacn [1] nacn [2]
soma_ih_type ihvcn [1] ihvcn [1] ihvcn [1] ihvcn [2]
soma_Cap 26.0 [1] 26.0 [1] 25.0 [1] 26.0 [2]
soma_na_vshift 4.3 [1] 4.3 [1] 4.3 [1] 4.3 [1]
soma_e_k -84 [1] -84 [1] -84 [1] -84 [2]
soma_e_na 50. [1] 50. [1] 50. [1] 50. [2]
soma_ih_eh -43 [1] -43 [1] -43 [1] -43 [2]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Uses channels from Rothman and Manis, 2003
Conductances are for Mouse bushy cells
Xie and Manis, 2013
Age "adult", Temperature=34C
Units are nS.
[2] Rothman and manis, 2003, model I-II
Some low-voltage K current, based on observations of
a single spike near threshold and regular firing for higher
currents (Xie and Manis, 2017)
""")
add_table_data('mGBC_channels', row_key='field', col_key='cell_type',
species='mouse', data=u"""
This table describes the ion channel densities (and voltage shifts if necessary)
for different cell types based on the Xie and Manis 2013 models for mouse.
This table is EXPERIMENTAL and should not be used for production-level simulations.
-----------------------------------------------------------------------------------------------------------------------------------
bushy-II
mGBC_name II
soma_na_gbar 1600. [1]
soma_kht_gbar 58.0 [1]
soma_klt_gbar 40.0 [1]
soma_ka_gbar 0.0 [1]
soma_ih_gbar 7.50 [1]
soma_leak_gbar 0.04 [1]
soma_leak_erev -65 [1]
soma_na_type jsrna [1]
soma_ih_type ihvcn [1]
soma_Cap 26.0 [1]
soma_na_vshift 4.3 [1]
soma_e_k -84 [1]
soma_e_na 50. [1]
soma_ih_eh -43 [1]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Uses channels from Rothman and Manis, 2003
Conductances are for Mouse bushy cells
Xie and Manis, 2013
Age "adult", Temperature=34C
Units are nS.
""")
add_table_data('POK_channels', row_key='field', col_key='cell_type',
species='rat', data=u"""
This table describes the ion channel densities and voltage shifts for rat DCN pyramidal cells,
from Kanold and Manis, 2001
The table includes 2 additiona variants
-----------------------------------------------------------------------------------------------------------------------------------
pyramidal
soma_napyr_gbar 350.0 [1]
soma_nap_gbar 0.
soma_kdpyr_gbar 80.0 [1]
soma_kcnq_gbar 0.
soma_kif_gbar 150.0 [1]
soma_kis_gbar 40.0 [1]
soma_ihpyr_gbar 2.8 [1]
soma_leak_gbar 2.8 [1]
soma_leak_erev -62.0 [1]
soma_e_na 50. [1]
soma_e_k -81.5 [1]
soma_e_h -43.0 [1]
soma_natype napyr
soma_Cap 12 [1]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Kanold and Manis, 1999, 2001, 2005
Age P11-14, Temperature=22C
Units are nS.
""")
add_table_data('CW_channels', row_key='field', col_key='cell_type',
species='mouse', data=u"""
This table describes the ion channel densities and voltage shifts
for a mouse carthweel cell model.
Ad-hoc model, based on a Purkinje cell model (ref [1]).
-----------------------------------------------------------------------------------------------------------------------------------
cartwheel
soma_narsg_gbar 500.0 [1]
soma_bkpkj_gbar 2.0
soma_kpkj_gbar 100. [1]
soma_kpkj2_gbar 50.
soma_kpkjslow_gbar 150 [1]
soma_kpksk_gbar 25.0 [1]
soma_lkpkj_gbar 5.0 [1]
soma_hpkj_gbar 5.0 [1]
soma_e_na 50. [1]
soma_e_k -80.0 [1]
soma_hpkj_eh -43.0 [1]
soma_lkpkj_e -65.0 [1]
soma_e_ca 50.
soma_na_type narsg
soma_pcabar 0.00015 [1]
soma_Dia 18
-----------------------------------------------------------------------------------------------------------------------------------
[1] Channels from Khaliq, Gouwens and Raman, J. Neurosci. 2003
Conductance levels modified.
""")
add_table_data('TV_channels', row_key='field', col_key='cell_type',
species='mouse', data=u"""
This table describes the ion channel densities and voltage shifts
for a mouse tuberculoventral cell model.
Ad-hoc model, based on the t-stellate cell model, but adjusted
to match the data from Kuo and Trussell.
-----------------------------------------------------------------------------------------------------------------------------------
TVmouse
soma_nacncoop_gbar 5800.0 [2]
soma_kht_gbar 400.0 [1]
soma_ihvcn_gbar 2.5 [2]
soma_ka_gbar 65.0 [1]
soma_leak_gbar 4.5 [1]
soma_leak_erev -72.0 [1]
soma_e_na 50. [1]
soma_e_k -81.5 [1]
soma_ihvcn_eh -43.0 [1]
soma_na_type nacncoop [2]
soma_Cap 35 [1]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Values obtained from brute force runs and comparision to
FI curve from Kuo, Lu and Trussell, J Neurophysiol. 2012 Aug 15;
108(4): 1186–1198.
[2] Cooperative sodium channel model, based on (see the mechanisms folder)
concepts and implementation similar to Oz et al. J.Comp. Neurosci. 39: 63, 2015,
and Huang et al., PloSOne 7:e37729, 2012.
""")
add_table_data('sgc_mouse_channels', row_key='field', col_key='cell_type',
species='mouse', data=u"""
This table describes the ion channel densities (and voltage shifts if necessary)
for SGC cells, based on
-----------------------------------------------------------------------------------------------------------------------------------
sgc-a sgc-bm
sgc_name a bm
soma_na_gbar 350. [2] 350. [2]
soma_kht_gbar 58.0 [1] 58.0 [1]
soma_klt_gbar 80.0 [1] 80.0 [1]
soma_ihap_gbar 3.0 [3] 0.0 [1]
soma_ihap_eh -41.0 [3] -41.0 [3]
soma_ihbm_gbar 0.0 [3] 3.0 [3]
soma_ihbm_eh -41.0 [3] -41.0 [3]
soma_leak_gbar 2.0 [1] 2.0 [1]
soma_leak_erev -65 [1] -65 [1]
soma_na_type jsrna [2] jsrna [2]
soma_Cap 12.0 [1] 12.0 [1]
soma_e_k -84 [1] -84 [1]
soma_e_na 50. [1] 50. [1]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Model is based on the mouse bushy cell model (XM13, above),
but with a fast sodium channel from Rothman et al, 1993. and Ih currents
from Liu et al. 2014
[2] Sodium channel from Rothman, Young and Manis, J Neurophysiol. 1993 Dec;70(6):2562-83.
[3] Ih Currents from Liu, Manis, Davis, J Assoc Res Otolaryngol. 2014 Aug;15(4):585-99.
doi: 10.1007/s10162-014-0446-z. Epub 2014 Feb 21.
Age "P10" (cultured SGC cells), Original data temperature=22C.
Units are nS.
""")
add_table_data('sgc_guineapig_channels', row_key='field', col_key='cell_type',
species='guineapig', data=u"""
This table describes the ion channel densities (and voltage shifts if necessary)
for a model SGC cell, which is based on a bushy cell with a different Na channel.
-----------------------------------------------------------------------------------------------------------------------------------
sgc-a sgc-bm
sgc_name a bm
soma_na_gbar 1000. [2] 1000. [2]
soma_kht_gbar 150.0 [1] 150.0 [1]
soma_klt_gbar 200.0 [1] 200.0 [1]
soma_ihap_gbar 3.0 [3] 0.0 [3]
soma_ihap_eh -41.0 [3] -41.0 [3]
soma_ihbm_gbar 0.0 [3] 3.0 [3]
soma_ihbm_eh -41.0 [3] -41.0 [3]
soma_leak_gbar 2.0 [1] 2.0 [1]
soma_leak_erev -65 [1] -65 [1]
soma_na_type jsrna [2] jsrna [2]
soma_Cap 12.0 [1] 12.0 [1]
soma_e_k -84 [1] -84 [1]
soma_e_na 50. [1] 50. [1]
-----------------------------------------------------------------------------------------------------------------------------------
[1] Model is based on the guinea pig bushy cell model (RM03, above),
but with a fast sodium channel from Rothman et al, 1993. and Ih currents
from Liu et al. 2014
[2] Sodium channel from Rothman, Young and Manis, J Neurophysiol. 1993 Dec;70(6):2562-83.
[3] Ih Currents from Liu, Manis, Davis, J Assoc Res Otolaryngol. 2014 Aug;15(4):585-99.
doi: 10.1007/s10162-014-0446-z. Epub 2014 Feb 21.
Age "P10" (cultured SGC cells), Temperature=22C.
Units are nS.
""")
add_table_data('MSO_principal_channels', row_key='field', col_key='cell_type',
species='guineapig', data=u"""
This table describes the ion channel densities
for a putative MSO principal neuron based on the original Rothman Manis 2003 model for bushy cells.
-----------------------------------------------------------------------------------------------------------------------------------
MSO-principal
MSO_name Principal
soma_na_gbar 1000. [1]
soma_kht_gbar 150.0 [1]
soma_klt_gbar 200.0 [1]
soma_ka_gbar 0.0 [1]
soma_ih_gbar 20.0 [1]
soma_leak_gbar 2.0 [1]
soma_leak_erev -65 [1]
soma_na_type nacn [1]
soma_ih_type ihvcn [1]
soma_Cap 12.0 [1]
soma_e_k -84 [1]
soma_e_na 50. [1]
soma_ih_eh -43 [1]
-----------------------------------------------------------------------------------------------------------------------------------
[1] This MSO neuron model is basied on Rothman and Manis, 2003 bushy cell, type II
Age "adult", Temperature=22C
Units are nS.
""")
|